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Items: 1 to 20 of 150

1.

jModelTest: phylogenetic model averaging.

Posada D.

Mol Biol Evol. 2008 Jul;25(7):1253-6. doi: 10.1093/molbev/msn083.

2.

Selection of models of DNA evolution with jModelTest.

Posada D.

Methods Mol Biol. 2009;537:93-112. doi: 10.1007/978-1-59745-251-9_5.

PMID:
19378141
3.
4.

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O.

Syst Biol. 2010 May;59(3):307-21. doi: 10.1093/sysbio/syq010.

PMID:
20525638
5.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.

Helaers R, Milinkovitch MC.

BMC Bioinformatics. 2010 Jul 15;11:379. doi: 10.1186/1471-2105-11-379.

6.

Selecting the best-fit model of nucleotide substitution.

Posada D, Crandall KA.

Syst Biol. 2001 Aug;50(4):580-601.

PMID:
12116655
8.

PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference.

Guindon S, Lethiec F, Duroux P, Gascuel O.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W557-9.

9.

Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.

Lanfear R, Calcott B, Ho SY, Guindon S.

Mol Biol Evol. 2012 Jun;29(6):1695-701. doi: 10.1093/molbev/mss020.

10.
11.

Does choice in model selection affect maximum likelihood analysis?

Ripplinger J, Sullivan J.

Syst Biol. 2008 Feb;57(1):76-85. doi: 10.1080/10635150801898920.

PMID:
18275003
12.

PAML 4: phylogenetic analysis by maximum likelihood.

Yang Z.

Mol Biol Evol. 2007 Aug;24(8):1586-91.

13.

Estimating maximum likelihood phylogenies with PhyML.

Guindon S, Delsuc F, Dufayard JF, Gascuel O.

Methods Mol Biol. 2009;537:113-37. doi: 10.1007/978-1-59745-251-9_6.

PMID:
19378142
14.

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.

Stamatakis A, Ludwig T, Meier H.

Bioinformatics. 2005 Feb 15;21(4):456-63.

15.

RDP2: recombination detection and analysis from sequence alignments.

Martin DP, Williamson C, Posada D.

Bioinformatics. 2005 Jan 15;21(2):260-2.

16.

In silico sequence evolution with site-specific interactions along phylogenetic trees.

Gesell T, von Haeseler A.

Bioinformatics. 2006 Mar 15;22(6):716-22.

17.

Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets.

Luo A, Qiao H, Zhang Y, Shi W, Ho SY, Xu W, Zhang A, Zhu C.

BMC Evol Biol. 2010 Aug 9;10:242. doi: 10.1186/1471-2148-10-242.

18.

Maximum-likelihood methods for phylogeny estimation.

Sullivan J.

Methods Enzymol. 2005;395:757-79.

PMID:
15865994
19.

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.

Olsen GJ, Matsuda H, Hagstrom R, Overbeek R.

Comput Appl Biosci. 1994 Feb;10(1):41-8.

PMID:
8193955
20.
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